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(-) Description

Title :  CRYSTAL STRUCTURES OF THE S504A MUTANT OF AN ISOLATED ABC-ATPASE IN COMPLEX WITH TNP-ADP
 
Authors :  C. Oswald, S. Jenewein, S. H. J. Smits, I. B. Holland, L. Schmitt
Date :  26 Oct 07  (Deposition) - 15 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Abc-Transporter, Nucleotide-Binding Doamin, Atpase, Atp-Binding, Hydrolase, Inner Membrane, Membrane, Transmembrane, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Oswald, S. Jenewein, S. H. J. Smits, I. B. Holland, L. Schmitt
Water-Mediated Protein-Fluorophore Interactions Modulate Th Affinity Of An Abc-Atpase/Tnp-Adp Complex
J. Struct. Biol. V. 162 85 2008
PubMed-ID: 18155559  |  Reference-DOI: 10.1016/J.JSB.2007.11.006

(-) Compounds

Molecule 1 - ALPHA-HEMOLYSIN TRANSLOCATION ATP-BINDING PROTEIN HLYB
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: ABC TRANSPORTER, RESIDUES UNP 467-707
    Gene: HLYB
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
112D1Ligand/Ion2',3'-O-[(1R,6R)-2,4,6-TRINITROCYCLOHEXA-2,4-DIENE-1,1-DIYL]ADENOSINE 5'-(TRIHYDROGEN DIPHOSPHATE)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:3 , HOH A:5 , HOH A:23 , HOH A:34 , HOH A:43 , HOH A:85 , HOH A:140 , HOH A:176 , HOH A:225 , HOH A:242 , TYR A:477 , PRO A:482 , ILE A:484 , GLY A:505 , SER A:506 , GLY A:507 , LYS A:508 , SER A:509 , THR A:510 , LYS A:513 , TYR A:519 , TRP A:540 , ARG A:543 , GLU A:689 , SER A:692 , GLU A:693 , PRO A:694BINDING SITE FOR RESIDUE 12D A 708

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B5J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3B5J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B5J)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ABC_TRANSPORTER_1PS00211 ABC transporters family signature.HLYBP_ECOLX606-620  1A:606-620

(-) Exons   (0, 0)

(no "Exon" information available for 3B5J)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:243
 aligned with HLYBP_ECOLX | P08716 from UniProtKB/Swiss-Prot  Length:707

    Alignment length:253
                                   464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704   
          HLYBP_ECOLX   455 YHGKLTLPEINGDITFRNIRFRYKPDSPVILDNINLSIKQGEVIGIVGRSGSGKSTLTKLIQRFYIPENGQVLIDGHDLALADPNWLRRQVGVVLQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTIVGEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRLSTVKNADRIIVMEKGKIVEQGKHKELLSEPESLYSYLYQLQSD 707
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .e----------eeeeeeeeee......eeeeeeeeeee...eeeee.....hhhhhhhhhh......eeeeee..ee....hhhhhhhheeee.........hhhhhhh......hhhhhhhhhhhh.hhhhhhh..hhhhh.........hhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhh..eeeee..hhhhhh...eeeeee..eeeeeehhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER--------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b5j A 465 HH----------DITFRNIRFRYKPDSPVILDNINLSIKQGEVIGIVGRAGSGKSTLTKLIQRFYIPENGQVLIDGHDLALADPNWLRRQVGVVLQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTIVGEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRLSTVKNADRIIVMEKGKIVEQGKHKELLSEPESLYSYLYQLQSD 707
                             |       -  |    474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704   
                             |        467                                                                                                                                                                                                                                                
                           466
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3B5J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3B5J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B5J)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HLYBP_ECOLX | P08716)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0042626    ATPase activity, coupled to transmembrane movement of substances    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to directly drive the active transport of a substance across a membrane.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
    GO:0030253    protein secretion by the type I secretion system    The process in which proteins are secreted into the extracellular milieu via the type I secretion system; secretion occurs in a continuous process without the distinct presence of periplasmic intermediates and does not involve proteolytic processing of secreted proteins.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0030256    type I protein secretion system complex    A complex of three secretory proteins that carry out secretion in the type I secretion system: an inner membrane transport ATPase (termed ABC protein for ATP-binding cassette), which provides the energy for protein secretion; an outer membrane protein, which is exported via the sec pathway; and a membrane fusion protein, which is anchored in the inner membrane and spans the periplasmic space.

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  HLYBP_ECOLX | P08716
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HLYBP_ECOLX | P08716: 1mt0 1xef 2ff7 2ffa 2ffb 2fgj 2fgk 2pmk

(-) Related Entries Specified in the PDB File

2pmk